I was told by Dave Dalke that my splitport would run on the OEM tune if I kept the stock injectors/MAF. He said the displacement wasn't much of an issue. On that note I'd be comfortable to say you can run the single-port 4.2 with the stock MN12 injectors and MAF from your engine and it will work.
Certainly, the MAF sends a voltage that the PCM uses a table called the MAF transfer function to determine how much air is entering the engine from. From that it determines how long to set the injector pulsewidth to in order to deliver the right amount of fuel using fuel flow characteristics information about the injectors in the program.
As long as the MAF transfer function matches the MAF sensor's characteristics then the right air value will be calculated. Likewise, as long as the injectors deliver the same amount of fuel in a given moment of time as the data in the PCM represents, the correct fuel delivery for the expected air quantity will be delivered.
The PCM also uses the MAF voltage, programmed engine displacement data, and RPM (along with other data, such as air and coolant temperature) to determine the spark advance. This will be off by a margin even with the right MAF and injectors, but will likely be close enough to run. If there's too much spark running premium fuel may help abate some of the pre-ignition issues; barring that the octane adjust plug may be pulled to pull more timing.
All in all though, the best solution really is to get the proper program for the vehicle since enough about the engine has changed significantly enough to necessitate a change to one of the big three (fuel, air, or spark) for best performance.